Efforts should start with the "highly iconic site" of the Umayyad mosque in the northern Syrian city of Aleppo, Bokova told a Paris conference on safeguarding the two countries' cultural riches.
"I believe that the Umayyad mosque, located within the World Heritage site of the old city of Aleppo, could and should be our starting point. It is not too late to take action," she said.
"We must create protected cultural zones around heritage sites, through stronger engagement with local actors."
More than three years into a bloody civil war, Syria's historical sites have suffered from widespread looting and damage, according to UNESCO.
The situation has worsened since Islamic State jihadists seized swathes of Syria and Iraq in recent months, destroying sites they consider idolatrous or heretical.
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In Iraq, the extremist group has destroyed shrines, churches and precious manuscripts in Mosul, Tikrit and other areas it controls and excavated sites to sell objects abroad.
Bokova condemned the attacks on cultural heritage and the black market dealings of looted items, calling them "part of a strategy of deliberate cultural cleansing of exceptional violence".
"I call on all parties involved in military operations to immediately stop all military use and targeting of cultural sites," Bokova said.
The minaret of Aleppo's famed Umayyad mosque was destroyed last year. The mosque, originally built in the 8th century and then rebuilt in the 13th century, has been left pockmarked by bullets.
The ancient covered market, or souk, has also been damaged by the intense fighting in Syria's second city.